Hi Sam, I need to add a more informative error message - the problem is that no valid BAF values are reaching the call to CNA (baf.dat is NULL). This could happen if the values of snp.ids or chrom.ids are invalid - these should all be integer values matching the contents of snpID and chromosome in the netCDF file. What values are you using for these arguments? You will need to have LRR in the intensity NetCDF file. A portion of the code downstream from the error you're getting uses LRR to filter potential anomalies. Stephanie On 5/30/13 12:30 PM, Sam Rose wrote: > Thank you for your previous help Stephanie. > > I am afraid I have another problem I can't seem to work out. > > I have gotten as far as reading in the BAlleleFreq and Geno files into > their respective ncdf formats. I only have the baf data in the intensity > ncdf file, do I need LRR too? When I run the anomDetectBAF() function it > gives me this error: > > > anom <- anomDetectBAF(blData, genoData, scan.ids=scan.ids, > chrom.ids=chrom.ids, snp.ids=snp.ids, centromere=centromeres.hg19) > Error in CNA(as.vector(baf.dat), chr, index, data.type = "logratio", > sampleid = snum) : > genomdat must be numeric > > I have checked and the data that I put in to the genotype data file was > numeric and present as well as the baf data. I'm wondering if you have > seen this error before and may potentially know what I can do to rectify? > > Thanks, > Sam > > > On Wed, Apr 24, 2013 at 12:01 AM, Stephanie M. Gogarten > <sdmorris at="" u.washington.edu="" <mailto:sdmorris="" at="" u.washington.edu="">> wrote: > > Hi Sam, > > Section 2 of the vignette "GWAS Data Cleaning" contains an example > of how to import raw illumina data of exactly this type into > GWASTools. The example data is contained in the package "GWASdata." > > If you have any further questions after reading the vignette, please > cc the bioconductor mailing list (bioconductor at r-project.org > <mailto:bioconductor at="" r-project.org="">). > > Section 7 may also be of use to you, as it deals with chromosome > anomaly detection. > > best wishes, > Stephanie > > > On 4/23/13 7:54 PM, Sam Rose wrote: > > Hi Stephanie, > > My name is Sam Rose and I am contacting you the GWASTools package in > Bioconductor of which it says you are the maintainer. > > I am trying to use the package to call mosaic CNVs in my samples and > can't seem to get it to work. > > I'm wondering if you have an example of the raw illumina data to > put in > there, and maybe examples of some of the things required in the > 'ncdfAddData' command (i.e. sample column, col.nums). I have > created the > shell ncdf file, but beyond that the headers and data formats > seem to be > giving me trouble so I just though I would ask. > > Our Illumina raw data files look like this: > SNP_NameChromosomePositionGC___ScoreAllele1_-_TopAllele2_- ___TopAllele1_-_ABAllele2_-___ABXYRaw_XRaw_YR_IlluminaTheta___Illumina bAllele_FreqLog_R___Ratio_IlluminaR_TrigTheta___TrigLog_R_Ratio_Trig > rs44772121720170.__38423407AAAA0.__393692269026780450.__0250 181864147452338333240.__41871045544152570.__040401312884379780.__00606 3504097364059-0.__6120798296992830.__394486390567453940.__063462233876 47508-0.__6182450719587295 > > Thanks for your help, > > Sam > > -- > ----- > *Sam Rose, Stanley Center Research Associate II > > Stanley Center for Psychiatric Research, The Broad Institute > 7 Cambridge Center, Cambridge, MA 02142* > 617.714.7853, srose at broadinstitute.org > <mailto:srose at="" broadinstitute.org=""> > <mailto:srose at="" broadinstitute.__org=""> <mailto:srose at="" broadinstitute.org="">> > > > > > -- > ----- > *Sam Rose, Stanley Center Research Associate II > Stanley Center for Psychiatric Research, The Broad Institute > 7 Cambridge Center, Cambridge, MA 02142* > 617.714.7853, srose at broadinstitute.org <mailto:srose at="" broadinstitute.org=""> >

GWASTools versions 1.6.2 (release) and 1.7.4 (devel) have better error messages in anomDectectBAF that may help diagnose where your error is occurring. These versions will be available through biocLite() tomorrow after ~10am Pacific time (or right now via svn). If you haven't figured it out already, try upgrading and report what error message you get. Stephanie On 5/30/13 1:43 PM, Stephanie M. Gogarten wrote: > Hi Sam, > > I need to add a more informative error message - the problem is that no > valid BAF values are reaching the call to CNA (baf.dat is NULL). This > could happen if the values of snp.ids or chrom.ids are invalid - these > should all be integer values matching the contents of snpID and > chromosome in the netCDF file. What values are you using for these > arguments? > > You will need to have LRR in the intensity NetCDF file. A portion of > the code downstream from the error you're getting uses LRR to filter > potential anomalies. > > Stephanie > > On 5/30/13 12:30 PM, Sam Rose wrote: >> Thank you for your previous help Stephanie. >> >> I am afraid I have another problem I can't seem to work out. >> >> I have gotten as far as reading in the BAlleleFreq and Geno files into >> their respective ncdf formats. I only have the baf data in the intensity >> ncdf file, do I need LRR too? When I run the anomDetectBAF() function it >> gives me this error: >> >> > anom <- anomDetectBAF(blData, genoData, scan.ids=scan.ids, >> chrom.ids=chrom.ids, snp.ids=snp.ids, centromere=centromeres.hg19) >> Error in CNA(as.vector(baf.dat), chr, index, data.type = "logratio", >> sampleid = snum) : >> genomdat must be numeric >> >> I have checked and the data that I put in to the genotype data file was >> numeric and present as well as the baf data. I'm wondering if you have >> seen this error before and may potentially know what I can do to rectify? >> >> Thanks, >> Sam >> >> >> On Wed, Apr 24, 2013 at 12:01 AM, Stephanie M. Gogarten >> <sdmorris at="" u.washington.edu="" <mailto:sdmorris="" at="" u.washington.edu="">> wrote: >> >> Hi Sam, >> >> Section 2 of the vignette "GWAS Data Cleaning" contains an example >> of how to import raw illumina data of exactly this type into >> GWASTools. The example data is contained in the package "GWASdata." >> >> If you have any further questions after reading the vignette, please >> cc the bioconductor mailing list (bioconductor at r-project.org >> <mailto:bioconductor at="" r-project.org="">). >> >> Section 7 may also be of use to you, as it deals with chromosome >> anomaly detection. >> >> best wishes, >> Stephanie >> >> >> On 4/23/13 7:54 PM, Sam Rose wrote: >> >> Hi Stephanie, >> >> My name is Sam Rose and I am contacting you the GWASTools >> package in >> Bioconductor of which it says you are the maintainer. >> >> I am trying to use the package to call mosaic CNVs in my >> samples and >> can't seem to get it to work. >> >> I'm wondering if you have an example of the raw illumina data to >> put in >> there, and maybe examples of some of the things required in the >> 'ncdfAddData' command (i.e. sample column, col.nums). I have >> created the >> shell ncdf file, but beyond that the headers and data formats >> seem to be >> giving me trouble so I just though I would ask. >> >> Our Illumina raw data files look like this: >> >> SNP_NameChromosomePositionGC___ScoreAllele1_-_TopAllele2_- ___TopAllele1_-_ABAllele2_-___ABXYRaw_XRaw_YR_IlluminaTheta___Illumina bAllele_FreqLog_R___Ratio_IlluminaR_TrigTheta___TrigLog_R_Ratio_Trig >> >> >> rs44772121720170.__38423407AAAA0.__393692269026780450.__02501818641 47452338333240.__41871045544152570.__040401312884379780.__006063504097 364059-0.__6120798296992830.__394486390567453940.__06346223387647508-0 .__6182450719587295 >> >> >> Thanks for your help, >> >> Sam >> >> -- >> ----- >> *Sam Rose, Stanley Center Research Associate II >> >> Stanley Center for Psychiatric Research, The Broad Institute >> 7 Cambridge Center, Cambridge, MA 02142* >> 617.714.7853, srose at broadinstitute.org >> <mailto:srose at="" broadinstitute.org=""> >> <mailto:srose at="" broadinstitute.__org="">> <mailto:srose at="" broadinstitute.org="">> >> >> >> >> >> -- >> ----- >> *Sam Rose, Stanley Center Research Associate II >> Stanley Center for Psychiatric Research, The Broad Institute >> 7 Cambridge Center, Cambridge, MA 02142* >> 617.714.7853, srose at broadinstitute.org <mailto:srose at="" broadinstitute.org=""> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor

Thank you for your previous help Stephanie. I am afraid I have another problem I can't seem to work out. I have gotten as far as reading in the BAlleleFreq and Geno files into their respective ncdf formats. I only have the baf data in the intensity ncdf file, do I need LRR too? When I run the anomDetectBAF() function it gives me this error: > anom <- anomDetectBAF(blData, genoData, scan.ids=scan.ids, chrom.ids=chrom.ids, snp.ids=snp.ids, centromere=centromeres.hg19) Error in CNA(as.vector(baf.dat), chr, index, data.type = "logratio", sampleid = snum) : genomdat must be numeric I have checked and the data that I put in to the genotype data file was numeric and present as well as the baf data. I'm wondering if you have seen this error before and may potentially know what I can do to rectify? Thanks, Sam On Wed, Apr 24, 2013 at 12:01 AM, Stephanie M. Gogarten < sdmorris@u.washington.edu> wrote: > Hi Sam, > > Section 2 of the vignette "GWAS Data Cleaning" contains an example of how > to import raw illumina data of exactly this type into GWASTools. The > example data is contained in the package "GWASdata." > > If you have any further questions after reading the vignette, please cc > the bioconductor mailing list (bioconductor@r-project.org). > > Section 7 may also be of use to you, as it deals with chromosome anomaly > detection. > > best wishes, > Stephanie > > > On 4/23/13 7:54 PM, Sam Rose wrote: > >> Hi Stephanie, >> >> My name is Sam Rose and I am contacting you the GWASTools package in >> Bioconductor of which it says you are the maintainer. >> >> I am trying to use the package to call mosaic CNVs in my samples and >> can't seem to get it to work. >> >> I'm wondering if you have an example of the raw illumina data to put in >> there, and maybe examples of some of the things required in the >> 'ncdfAddData' command (i.e. sample column, col.nums). I have created the >> shell ncdf file, but beyond that the headers and data formats seem to be >> giving me trouble so I just though I would ask. >> >> Our Illumina raw data files look like this: >> SNP_NameChromosomePositionGC_**ScoreAllele1_-_TopAllele2_-_** >> TopAllele1_-_ABAllele2_-_**ABXYRaw_XRaw_YR_IlluminaTheta_** >> IlluminabAllele_FreqLog_R_**Ratio_IlluminaR_TrigTheta_** >> TrigLog_R_Ratio_Trig >> rs44772121720170.**38423407AAAA0.**393692269026780450.** >> 0250181864147452338333240.**41871045544152570.**040401312884379780.** >> 006063504097364059-0.**6120798296992830.**394486390567453940.** >> 06346223387647508-0.**6182450719587295 >> >> Thanks for your help, >> >> Sam >> >> -- >> ----- >> *Sam Rose, Stanley Center Research Associate II >> >> Stanley Center for Psychiatric Research, The Broad Institute >> 7 Cambridge Center, Cambridge, MA 02142* >> 617.714.7853, srose@broadinstitute.org <mailto:srose@broadinstitute.**org<srose@broadinstitute.org> >> > >> >> -- ----- *Sam Rose, Stanley Center Research Associate II Stanley Center for Psychiatric Research, The Broad Institute 7 Cambridge Center, Cambridge, MA 02142* 617.714.7853, srose@broadinstitute.org [[alternative HTML version deleted]]

Looks like there was some problems reading the file in on my end, some chromosomes didn't make it in probably from a preprocessing step on my end. I'll let you know if I can't rectify. Thanks again for the help, Sam On Thu, May 30, 2013 at 4:43 PM, Stephanie M. Gogarten < sdmorris@u.washington.edu> wrote: > Hi Sam, > > I need to add a more informative error message - the problem is that no > valid BAF values are reaching the call to CNA (baf.dat is NULL). This > could happen if the values of snp.ids or chrom.ids are invalid - these > should all be integer values matching the contents of snpID and chromosome > in the netCDF file. What values are you using for these arguments? > > You will need to have LRR in the intensity NetCDF file. A portion of the > code downstream from the error you're getting uses LRR to filter potential > anomalies. > > Stephanie > > > On 5/30/13 12:30 PM, Sam Rose wrote: > >> Thank you for your previous help Stephanie. >> >> I am afraid I have another problem I can't seem to work out. >> >> I have gotten as far as reading in the BAlleleFreq and Geno files into >> their respective ncdf formats. I only have the baf data in the intensity >> ncdf file, do I need LRR too? When I run the anomDetectBAF() function it >> gives me this error: >> >> > anom <- anomDetectBAF(blData, genoData, scan.ids=scan.ids, >> chrom.ids=chrom.ids, snp.ids=snp.ids, centromere=centromeres.hg19) >> Error in CNA(as.vector(baf.dat), chr, index, data.type = "logratio", >> sampleid = snum) : >> genomdat must be numeric >> >> I have checked and the data that I put in to the genotype data file was >> numeric and present as well as the baf data. I'm wondering if you have >> seen this error before and may potentially know what I can do to rectify? >> >> Thanks, >> Sam >> >> >> On Wed, Apr 24, 2013 at 12:01 AM, Stephanie M. Gogarten >> <sdmorris@u.washington.edu <mailto:sdmorris@u.washington.**edu<sdmorris@u.washington.edu="">>> >> wrote: >> >> Hi Sam, >> >> Section 2 of the vignette "GWAS Data Cleaning" contains an example >> of how to import raw illumina data of exactly this type into >> GWASTools. The example data is contained in the package "GWASdata." >> >> If you have any further questions after reading the vignette, please >> cc the bioconductor mailing list (bioconductor@r-project.org >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org="">>). >> >> >> Section 7 may also be of use to you, as it deals with chromosome >> anomaly detection. >> >> best wishes, >> Stephanie >> >> >> On 4/23/13 7:54 PM, Sam Rose wrote: >> >> Hi Stephanie, >> >> My name is Sam Rose and I am contacting you the GWASTools package >> in >> Bioconductor of which it says you are the maintainer. >> >> I am trying to use the package to call mosaic CNVs in my samples >> and >> can't seem to get it to work. >> >> I'm wondering if you have an example of the raw illumina data to >> put in >> there, and maybe examples of some of the things required in the >> 'ncdfAddData' command (i.e. sample column, col.nums). I have >> created the >> shell ncdf file, but beyond that the headers and data formats >> seem to be >> giving me trouble so I just though I would ask. >> >> Our Illumina raw data files look like this: >> SNP_NameChromosomePositionGC__**_ScoreAllele1_- _TopAllele2_-__** >> _TopAllele1_-_ABAllele2_-___**ABXYRaw_XRaw_YR_IlluminaTheta_** >> __IlluminabAllele_FreqLog_R___**Ratio_IlluminaR_TrigTheta___** >> TrigLog_R_Ratio_Trig >> rs44772121720170.__**38423407AAAA0.__**393692269026780450.__** >> 0250181864147452338333240.__**41871045544152570.__**040401312884379 780.__ >> **006063504097364059-0.__**6120798296992830.__**394486390567453940. __** >> 06346223387647508-0.__**6182450719587295 >> >> >> Thanks for your help, >> >> Sam >> >> -- >> ----- >> *Sam Rose, Stanley Center Research Associate II >> >> Stanley Center for Psychiatric Research, The Broad Institute >> 7 Cambridge Center, Cambridge, MA 02142* >> 617.714.7853, srose@broadinstitute.org >> <mailto:srose@broadinstitute.**org <srose@broadinstitute.org="">> >> <mailto:srose@broadinstitute._**_org>> <mailto:srose@broadinstitute.**org <srose@broadinstitute.org="">>> >> >> >> >> >> >> -- >> ----- >> *Sam Rose, Stanley Center Research Associate II >> Stanley Center for Psychiatric Research, The Broad Institute >> 7 Cambridge Center, Cambridge, MA 02142* >> 617.714.7853, srose@broadinstitute.org <mailto:srose@broadinstitute.**org<srose@broadinstitute.org> >> > >> >> -- ----- *Sam Rose, Stanley Center Research Associate II Stanley Center for Psychiatric Research, The Broad Institute 7 Cambridge Center, Cambridge, MA 02142* 617.714.7853, srose@broadinstitute.org [[alternative HTML version deleted]]